Folding and Intrinsic Disorder of the Receptor Tyrosine Kinase KIT Insert Domain Seen by Conventional Molecular Dynamics Simulations

The kinase insert domain (KID) of RTK KIT is the key recruitment region for downstream signalling proteins. KID, studied by molecular dynamics simulations as a cleaved polypeptide and as a native domain fused to KIT, showed intrinsic disorder represented by a set of heterogeneous conformations. The accurate atomistic models showed that the helical fold of KID is mainly sequence dependent. However, the reduced fold of the native KID suggests that its folding is allosterically controlled by the kinase domain. The tertiary structure of KID represents a compact array of highly variable α- and 3₁₀-helices linked by flexible loops playing a principal role in the conformational diversity. The helically folded KID retains a collapsed globule-like shape due to non-covalent interactions associated in a ternary hydrophobic core. The free energy landscapes constructed from first principles—the size, the measure of the average distance between the conformations, the amount of helices and the solvent-accessible surface area—describe the KID disorder through a collection of minima (wells), providing a direct evaluation of conformational ensembles. We found that the cleaved KID simulated with restricted N- and C-ends better reproduces the native KID than the isolated polypeptide. We suggest that a cyclic, generic KID would be best suited for future studies of KID f post-transduction effects.     

Detection of Melamine in Gluten,Chicken Feed,and Processed Foods Using Surface Enhanced Raman Spectroscopy and HPLC

ABSTRACT: Melamine, a nitrogen‐rich chemical, was implicated in pet and human food recalls in 2007, which caused enormous economic losses to the food industry. In this study, melamine concentration in wheat gluten, chicken feed, and processed foods (that is, cake and noodle) was measured by surface enhanced Raman spectroscopy (SERS) in combination with SERS‐active substrates. SERS was able to rapidly detect 0.1% melamine in wheat gluten, 0.05% in chicken feed, 0.05% in cakes, and 0.07% in noodle, respectively. A partial least squares (PLS) model was established for the quantification of melamine in foods by SERS: R= 0.90, RMSEP = 0.33. In addition, SERS results were verified by HPLC analysis based on a simplified FDA method. Compared with HPLC, the SERS method is much faster and simpler, requires minimum sample preparation, but still yields satisfactory qualitative and quantitative results. These results demonstrate that it is an applicable approach to use SERS to screen foods, eliminate presumptive negative samples of melamine contamination from the sample population, and then verify presumptive positive samples using HPLC protocols. Combining these 2 methods could provide a more rapid and cost‐effective way for monitoring melamine contamination in increasingly large numbers of imported foods and feed products.     

Development of a microfabricated optical bend loss sensor for distributive pressure measurement.

A flexible high-resolution sensor capable of measuring the distribution of pressure beneath the foot via a microfabricated optical waveguide system is presented. The uniqueness of the system is in its batch fabrication process, which involves a microfabrication molding technique with polydimethylsiloxane (PDMS) as the optical medium. The sensor manufacturing technique is described in detail, the optical performance of the waveguides is quantified and the effect of using a matching fluid to improve fiber-coupling efficiency is demonstrated. Mechanical loading tests were performed on a 4 x 4 array with a 2-mm spacing between sensing elements. Loading displacement curves were obtained using a 0 to 0.4 mm triangle loading profile. A force of 0.28 N applied to one of the sensing elements produced a displacement of a 0.325 mm and 39% change in the output light intensity. Multiple loadings were conducted to demonstrate the repeatability of the sensor. A force image algorithm with a two-layer neural network system was used to identify four load magnitudes and four different shaped applicators. All four shapes were successfully identified with the neural network.     

Shells of crystal field symmetries evidenced in oxide nano-crystals

By the use of a point charge model based on the Judd-Ofelt transition theory, the luminescence from Eu(3+) ions embedded in Gd(2)O(3) clusters is calculated and compared to the experimental data. The main result of the numerical study is that without invoking any other mechanisms such as crystal disorder, the pure geometrical argument of the symmetry breaking induced by the particle surface has an influence on the energy level splitting. The modifications are also predicted to be observable in realistic conditions where unavoidable size dispersion has to be taken into account. The emission spectrum results from the contribution of three distinct regions; a cluster core, a cluster shell and the very surface, the latter being almost completely quenched in realistic conditions. Eventually, by detailing the spectra of the ions embedded at different positions in the cluster we get an estimate of about 0.5 nm for the extent of the crystal field induced Stark effect. Due to the similarity between Y (2)O(3) and Gd(2)O(3), these results also apply to Eu(3+) doped Y(2)O(3) nanoparticles.     

Composite part design based on numerical simulation of the manufacturing process

In aeronautics, the decreased density of structural components is a major factor to consider in order to satisfy economic, environmental, and technical requirements. Using composite materials is justifying good weight to mechanical strength compromise. Mechanical strength depends on shapes, dimensions, and materials defined at the design stage and in manufacturing and assembling process of the part. In this article, a general method is proposed to evaluate the performance of the design choices based on the failure risk of an assembled part. This evaluation integrates manufacturing deviations from the shaping operation (resin transfer molding). Three criteria are derived from numerical simulations of RTM process and assembly phase. These criteria assist the designer early in the design cycle to appreciate the consequences of manufacturing choices on the mechanical strength of an assembled part. The approach will be applied to an airplane component.     

Influence of the oxygen pretreatment on the CO2 reforming of methane on Ni/β-SiC catalyst

The influence of the O₂ pretreatment on the CO₂ reforming of methane to synthesis gas has been investigated with Ni catalysts supported on β-SiC extrudate. The structure and properties of the catalysts were characterised by SEM, TEM and XRD techniques. The pretreatment of the catalyst by a mixture of CO₂ and O₂ significantly improves the catalytic activity for the CO₂ reforming. On the Ni 5 wt.% supported on β-SiC catalyst, the CH₄ conversion has reached 90% with the O₂ pretreatment instead of 80% by direct activation under CO₂/CH₄ mixture. The oxygen pretreatment seems to stabilize the metallic nickel phase instead of NiSi₂.     

Fe2O3/β-SiC: A new high efficient catalyst for the selective oxidation of H2S into elemental sulfur

Over the last decades, sulfur recovery from the H₂S-containing acid gases (issued from oil refineries or natural gas plants) has become more and more important due to the ever increasing standards of efficiency required by environmental protection pressures. The H₂S-tail gas was directly oxidized by oxygen to yield elemental sulfur. A significant improvement of the H₂S conversion and selectivity has been developed, however, the support which is the core of the process still needs to be improved. Recently, β-SiC has been reported to be an efficient and selective catalyst support for the H₂S-to-S reaction. One expected reason for this superior yield should be due to the high thermal conductivity of the support. The high thermal conductivity of the silicon carbide plays an important role in the maintenance of the high selectivity by avoiding the formation of hot spots on the catalyst surface which could favor secondary reactions. On the other hand, insulator supports such as alumina exhibit a poor selectivity due to catalyst surface temperature runaway.     

Fun sheet matching: towards automatic block decomposition for hexahedral meshes

Depending upon the numerical approximation method that may be implemented, hexahedral meshes are frequently preferred to tetrahedral meshes. Because of the layered structure of hexahedral meshes, the automatic generation of hexahedral meshes for arbitrary geometries is still an open problem. This layered structure usually requires topological modifications to propagate globally, thus preventing the general development of meshing algorithms such as Delaunay??s algorithm for tetrahedral meshes or the advancing-front algorithm based on local decisions. To automatically produce an acceptable hexahedral mesh, we claim that both global geometric and global topological information must be taken into account in the mesh generation process. In this work, we propose a theoretical classification of the layers or sheets participating in the geometry capture procedure. These sheets are called fundamental, or fun-sheets for short, and make the connection between the global layered structure of hexahedral meshes and the geometric surfaces that are captured during the meshing process. Moreover, we propose a first generation algorithm based on fun-sheets to deal with 3D geometries having 3- and 4-valent vertices.     

Topological modifications of hexahedral meshes via sheet operations: a theoretical study

Over the years, there have been a number of practical studies with working definitions of ‘mesh’ as related to computational simulation, however, there are only a few theoretical papers with formal definitions of mesh. Algebraic topology papers are available that define tetrahedral meshes in terms of simplices. Algebraic topology and polytope theory has also been utilized to define hexahedral meshes. Additional literature is also available describing particular properties of the dual of a mesh. In this paper, we give several formal definitions in relation to hexahedral meshes and the dual of hexahedral meshes. Our main goal is to provide useful, understandable and minimal definitions specifically for computer scientists or mathematicians working in hexahedral meshing. We also extend these definitions to some useful classifications of hexahedral meshes, including definitions for ‘fundamental’ hexahedral meshes and ‘minimal’ hexahedral meshes.